I was a bit shaken to read this short article, Submit It Again! Learning From Rejected Manuscripts (Campbell et al. 2022), recently posted on Mastodon by open-access legend Peter Suber.

For example:

Journals may reject manuscripts because the paper is not in the scope of the journal, because they recently published a similar article, because the formatting of the article is incorrect, or because the paper is not noteworthy. In addition, editors may reject a paper expecting authors to make their work more compelling.

Let’s pick this apart a bit.

“Because they recently published a similar article”? What is this nonsense. Does the Journal of Vertebrate Paleontology reject a paper on, say, ornithopod ontogeny because “we published something on ornithopod ontogeny a few months ago”? No, it doesn’t because it’s a serious journal.

“Because the formatting of the article is incorrect”? What is this idiocy? If the formatting is incorrect, the job of the publisher is to correct it. That’s literally what they’re there for.

“Expecting authors to make their work more compelling”. This is code for sexing up the results, maybe dropping that inconvenient outlier, getting p below 0.05 … in short, fraud. The very last thing we need more of.

Elsewhere this paper suggests:

… adjusting an original research paper to a letter to the editor or shifting the focus to make the same content into a commentary or narrative essay.

Needless to say, this is putting the cart before the horse. Once we start prioritising what kind of content a journal would like to have ahead of what our work actually tells us, we’re not scientists any more.

Then there is this:

Most manuscripts can eventually Ynd a home in a PubMed-indexed journal if the authors continually modify the manuscript to the specifications of the editors.

I’m not saying this is incorrect. I’m not even saying it’s not good advice. But I worry about the attitude that it communicates — that editors are capricious gods whose whims are to be satisfied. Editors should be, and good editors are, partners in the process of bringing a work to publication, not barriers.

Next up:

Studies confirming something already well known and supported might not be suitable for publication, but looking for a different perspective or a new angle to make it a new contribution to the literature may be useful.

In other words, if you run an experiment, however well you do the work and however well you write the paper, you should expect to have it rejected if the result doesn’t excite the editor. But if you can twist it into something that does excite the editor, you might be OK. Is this really how we want to encourage researchers to behave?

I’ve seen studies like this. I have seen projects that set out to determine how tibia shape correlates with lifestyle in felids, find out the rather important fact that there is no correlation, and instead report the Principle Component 1, which explains 4.2% of the morphological difference, sort of shows a slight grouping if you squint hard and don’t mind all your groups overlapping. (Note: all details changed to protect the guilty. I know nothing of felid tibiae.) I don’t wish to see more such reporting. I want to know what a study actually showed, not what an editor thought might be exciting.

But here is why I am so unhappy about this paper.

It’s that the authors seem so cheerful about all this. That they serenely accept it as a law of the universe that perfectly good papers can be rejected for the most spurious of reasons, and that the proper thing to do is smile broadly and take your ass to the next ass-kicking station.

It doesn’t seem to occur to them that there are other ways of doing scientific communication: ways that are constructive rather than adversarial, ways the aim to get at the truth rather than aiming at being discussed in a Malcolm Gladwell book[1], ways that make the best use of researchers’ work instead of discarding what is inconvenient.

Folks, we have to do better. Those of us in senior positions have to make sure we’re not teaching out students that the psychopathic systems we had to negotiate are a law of the universe.

References

Campbell, Kendall M., Judy C. Washington, Donna Baluchi and José E. Rodríguez. 2022. Submit It Again! Learning From Rejected Manuscripts. PRiMER. 6:42. doi:10.22454/PRiMER.2022.715584

Notes

  1. I offer the observation that any finding reported and discussed in a Malcolm Gladwell book seems to have about an 80% chance of being shown to be incorrect some time in the next ten years. In the social sciences, particularly, a good heuristic for guessing whether or not a given result is going to replicate is to ask: has it been in a Gladwell book?

 

Today marks the one-month anniversary of my and Matt’s paper in Qeios about why vertebral pneumaticity in sauropods is so variable. (Taylor and Wedel 2021). We were intrigued to publish on this new platform that supports post-publication peer-review, partly just to see what happened.

Taylor and Wedel (2021: figure 3). Brontosaurus excelsus holotype YPM 1980, caudal vertebrae 7 and 8 in right lateral view. Caudal 7, like most of the sequence, has a single vascular foramen on the right side of its centrum, but caudal 8 has two; others, including caudal 1, have none.

So what has happened? Well, as I write this, the paper has been viewed 842 times, downloaded a healthy 739 times, and acquired an altmetric score 21, based rather incestuously on two SV-POW! blog-posts, 14 tweets and a single Mendeley reader.

What hasn’t happened is even a single comment on the paper. Nothing that could be remotely construed as a post-publication peer-review. And therefore no progress towards our being able to count this as a peer-reviewed publication rather than a preprint — which is how I am currently classifying it in my publications list.

This, despite our having actively solicited reviews both here on SV-POW!, in the original blog-post, and in a Facebook post by Matt. (Ironically, the former got seven comments and the latter got 20, but the actual paper none.)

I’m not here to complain; I’m here to try to understand.

On one level, of course, this is easy to understand: writing a more-than-trivial comment on a scholarly article is work, and it garners very little of the kind of credit academics care about. Reputation on the Qeios site is nice, in a that-and-two-bucks-will-buy-me-a-coffee kind of way, but it’s not going to make a difference to people’s CVs when they apply for jobs and grants — not even in the way that “Reviewed for JVP” might. I completely understand why already overworked researchers don’t elect to invest a significant chunk of time in voluntarily writing a reasoned critique of someone else’s work when they could be putting that time into their own projects. It’s why so very few PLOS articles have comments.

On the other hand, isn’t this what we always do when we write a solicited peer-review for a regular journal?

So as I grope my way through this half-understood brave new world that we’re creating together, I am starting to come to the conclusion that — with some delightful exceptions — peer-review is generally only going to happen when it’s explicitly solicited by a handling editor, or someone with an analogous role. No-one’s to blame for this: it’s just reality that people need a degree of moral coercion to devote that kind of effort to other people’s project. (I’m the same; I’ve left almost no comments on PLOS articles.)

Am I right? Am I unduly pessimistic? Is there some other reason why this paper is not attracting comments when the Barosaurus preprint did? Teach me.

References

 

We’ve noted many times over the years how inconsistent pneumatic features are in sauropod vertebra. Fossae and formamina vary between individuals of the same species, and along the spinal column, and even between the sides of individual vertebrae. Here’s an example that we touched on in Wedel and Taylor (2013), but which is seen in all its glory here:

Taylor and Wedel (2021: Figure 5). Giraffatitan brancai tail MB.R.5000, part of the mounted skeleton at the Museum für Naturkunde Berlin. Caudal vertebrae 24–26 in left lateral view. While caudal 26 has no pneumatic features, caudal 25 has two distinct pneumatic fossae, likely excavated around two distinct vascular foramina carrying an artery and a vein. Caudal 24 is more shallowly excavated than 25, but may also exhibit two separate fossae.

But bone is usually the least variable material in the vertebrate body. Muscles vary more, nerves more again, and blood vessels most of all. So why are the vertebrae of sauropods so much more variable than other bones?

Our new paper, published today (Taylor and Wedel 2021) proposes an answer! Please read it for the details, but here’s the summary:

  • Early in ontogenly, the blood supply to vertebrae comes from arteries that initially served the spinal cord, penetrating the bone of the neural canal.
  • Later in ontegeny, additional arteries penetrate the centra, leaving vascular foramina (small holes carrying blood vessels).
  • This hand-off does not always run to completion, due to the variability of blood vessels.
  • In extant birds, when pneumatic diverticula enter the bone they do so via vascular foramina, alongside blood vessels.
  • The same was probaby true in sauropods.
  • So in vertebrae that got all their blood supply from vascular foramina in the neural canal, diverticula were unable to enter the centra from the outside.
  • So those centra were never pneumatized from the outside, and no externally visible pneumatic cavities were formed.

Somehow that pretty straightforward argument ended up running to eleven pages. I guess that’s what you get when you reference your thoughts thoroughly, illustrate them in detail, and discuss the implications. But the heart of the paper is that little bullet-list.

Taylor and Wedel (2021: Figure 6). Domestic duck Anas platyrhynchos, dorsal vertebrae 2–7 in left lateral view. Note that the two anteriormost vertebrae (D2 and D3) each have a shallow pneumatic fossa penetrated by numerous small foramina.

(What is the relevance of these duck dorsals? You will need to read the discussion in the paper to find out!)

Our choice of publication venue

The world moves fast. It’s strange to think that only eleven years ago my Brachiosaurus revision (Taylor 2009) was in the Journal of Vertebrate Palaeontology, a journal that now feels very retro. Since then, Matt and I have both published several times in PeerJ, which we love. More recently, we’ve been posting preprints of our papers — and indeed I have three papers stalled in peer-review revisions that are all available as preprints (two Taylor and Wedels and a single sole-authored one). But this time we’re pushing on even further into the Shiny Digital Future.

We’ve published at Qeios. (It’s pronounced “chaos”, but the site doesn’t tell you that; I discovered it on Twitter.) If you’ve not heard of it — I was only very vaguely aware of it myself until this evening — it runs on the same model as the better known F1000 Research, with this very important difference: it’s free. Also, it looks rather slicker.

That model is: publish first, then filter. This is the opposite of the traditional scholarly publishing flow where you filter first — by peer reviewers erecting a series of obstacles to getting your work out — and only after negotiating that course to do get to see your work published. At Qeios, you go right ahead and publish: it’s available right off the bat, but clearly marked as awaiting peer-review:

And then it undergoes review. Who reviews it? Anyone! Ideally, of course, people with some expertise in the relevant fields. We can then post any number of revised versions in response to the reviews — each revision having its own DOI and being fixed and permanent.

How will this work out? We don’t know. It is, in part, an experiment. What will make it work — what will impute credibility to our paper — is good, solid reviews. So if you have any relevant expertise, we do invite you to get over there and write a review.

And finally …

Matt noted that I first sent him the link to the Qeios site at 7:44 pm my time. I think that was the first time he’d heard of it. He and I had plenty of back and forth on where to publish this paper before I pushed on and did it at Qeios. And I tweeted that our paper was available for review at 8:44 — one hour exactly after Matt learned that the venue existed. Now here we are at 12:04 my time, three hours and 20 minutes later, and it’s already been viewed 126 times and downloaded 60 times. I think that’s pretty awesome.

References

  • Taylor, Michael P. 2009. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrate Paleontology 29(3):787-806. [PDF]
  • Taylor, Michael P., and Mathew J. Wedel. 2021. Why is vertebral pneumaticity in sauropod dinosaurs so variable? Qeios 1G6J3Q. doi: 10.32388/1G6J3Q [PDF]
  • Wedel, Mathew J., and Michael P. Taylor 2013b. Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus. PLOS ONE 8(10):e78213. 14 pages. doi: 10.1371/journal.pone.0078213 [PDF]

Here’s an odd thing. Over and over again, when a researcher is mistreated by a journal or publisher, we see them telling their story but redacting the name of the journal or publisher involved. Here are a couple of recent examples.

First, Daniel A. González-Padilla’s experience with a journal engaging in flagrant citation-pumping, but which he declines to name:

Interesting highlight after rejecting a paper I submitted.
Is this even legal/ethical?
EDITOR-IN-CHIEF’S COMMENT REGARDING THE INCLUSION OF REFERENCES TO ARTICLES IN [REDACTED]
Please note that if you wish to submit a manuscript to [REDACTED] in future, we would prefer that you cite at least TWO articles published in our journal WITHIN THE LAST TWO YEARS. This is a polict adopted by several journals in the urology field. Your current article contains only ONE reference to recent articles in [REDACTED].

We know from a subsequent tweet that the journal is published by Springer Nature, but we don’t know the name of the journal itself.

And here is Waheed Imran’s experience of editorial dereliction:

I submitted my manuscript to a journal back in September 2017, and it is rejected by the journal on September 6, 2020. The reason of rejection is “reviewers declined to review”, they just told me this after 3 years, this is how we live with rejections. @AcademicChatter
@PhDForum

My, my question is, why in such situations do we protect the journals in question? In this case, I wrote to Waheed urging him to name the journal, and he replied saying that he will do so once an investigation is complete. But I find myself wondering why we have this tendency to protect guilty journals in the first place?

Thing is, I’ve done this myself. For example, back in 2012, I wrote about having a paper rejected from “a mid-to-low ranked palaeo journal” for what I considered (and still consider) spurious reasons. Why didn’t I name the journal? I’m not really sure. (It was Palaeontologia Electronica, BTW.)

In cases like my unhelpful peer-review, it’s not really a big deal either way. In cases like those mentioned in the tweets above, it’s a much bigger issue, because those (unlike PE) are journals to avoid. Whichever journal sat on a submission for three years before rejecting it because it couldn’t find reviewers is not one that other researchers should waste their time on in the future — but how can they avoid it if they don’t know what journal it is?

So what’s going on? Why do we have this widespread tendency to protect the guilty?

Update (13 September 2021)

One year later, Waheed confirms that the journal in question not only did not satisfactorily resolve his complaint, it didn’t even respond to his message. At this stage, there really is no point in protecting the journal that has behaved so badly, so Waheed outed it: it’s Scientia Iranica. Avoid.

Publishers provide certain services (peer-review management, typesetting, brand badges, sometimes proof-reading or copy-editing, archiving, indexing) to the scholarly community.

Those services are of greater and lesser value, provided at higher and lower levels of quality, and cost greater and lesser amounts. Of course, we in the scholarly community want high-value, high-quality low-cost services. This is true whether the publisher in question is a multinational corporation with a multi-billion-dollar turnover, or a tiny boutique press run on a non-profit basis for the sheer love of the process.

Since the scholarly community (researchers, authors, peer-reviewers, academic editors, etc.) is spending money in exchange for publication services, and since publishers are providing publication services in exchange for money, it is clear that the goals of these two groups cannot be aligned. Any money that the scholarly community can save on publication costs is income lost to publishers; and any additional money that publishers can charge for their services is money lost to the scholarly community. I hope that so far, this is uncontroversial.

In the same way, if you sell me a second-hand car, then however well you and I might get on in civilian life — we might support the same football team, drink the same beer, discuss the same novelists, watch the same films — then for the purposes of that transaction, what is good for you (a high price) is bad for me; and vice versa. Note that in saying this I am not condemning or even criticising you. I am just stating a fact about transactions.

Now, suppose my wife and I sit down and decide that we need to buy a new car. We consider Hondas, Fords and Fiats. We weigh up various models on their merits, compare their prices with their features, and reach a decision on what we want to buy and how much we’re prepared to spend. We then approach the various Honda dealers (or, as we may have decided, Ford dealers or Fiat dealers). We negotiate with them to agree a price that we are happy with for a model that is in good enough condition. Different dealers compete with each other to win our custom by offering good cars at a low price. This is a functioning market.

What we don’t do is invite all the dealers to come and join us in our initial conversation. When my wife and I are discussing how important it is to us that our new car has variable-speed intermittent windscreen-wipers, we have that discussion in an environment quite free of car dealers telling us how great Fiat’s intermittent-wipe feature is. How could we possibly reach a coherent decision on what our own requirements are if we’re bombarded by the claims — some competing, some in collusion — of all the car dealers? And how can we think sensibly about what we’re prepared to spend if we’re surrounded by the dealers’ defences of the various financing arrangements they offer?

So in the same way, I feel that the scholarly community needs to figure out what publication services it needs, free of the influence of publishers who (and again this is not a criticism) have their own agenda. Then, when we know what we want, we can go to the publishers who offer the kinds of services we’re interested in, and invite them compete for our business on the basis of features and price.

But involving them in the initial what-we-want discussion can only lead to confusion, and a compromised outcome. Which is what we’ve seen for the last 50 years. This was the fatal flaw that led to the deeply flawed Finch Report and to the erosion of the RCUK’s initially very progressive OA policy.

As a side-note: my wife and I may end up deciding we don’t need a car at all: we might decide we can walk, or cycle, or take public transport. Car dealers would hate that: they would advocate against such an outcome with all their might if they were involved in that discussion. Which is why they can’t be.

 


Note. This post is adapted from a message to the Open Scholarship Initiative mailing list.

Yesterday I announced that our new paper on Barosaurus was up as a PeerJ preprint and invited feedback.

I woke up this morning to find its third substantial review waiting for me.

That means that this paper has now accumulated as much useful feedback in the twenty-seven hours since I submitted it as any previous submission I’ve ever made.

xx

Taylor and Wedel (2013b: figure 7). Barosaurus lentus holotype YPM 429, Vertebra S (C?12). Left column from top to bottom: dorsal, right lateral and ventral views; right column: anterior view. Inset shows displaced fragment of broken prezygapophysis. Note the narrow span across the parapophyses in ventral view, and the lack of damage to the ventral surface of the centrum which would indicate transverse crushing.

It’s worth reviewing the timeline here:

  • Monday 23rd September, 1:19 am: I completed the submission process.
  • 7:03 am: the preprint was published. It took less than six hours.
  • 10:52 am: received a careful, detailed review from Emanuel Tschopp. It took less than four hours from publication, and so of course less than ten from submission.
  • About 5:00 pm: received a second review, this one from Mark Robinson. (I don’t know the exact time because PeerJ’s page doesn’t show an actual timestamp, just “21 hours ago”.)
  • Tuesday 24th September, about 4:00 am: received a third review, this from ceratopsian-jockey and open-science guru Andy Farke.

Total time from submission to receiving three substantial reviews: about 27 hours.

It’s worth contrasting that with the times taken to get from submission to the receipt of reviews — usually only two of them — when going through the traditional journal route. Here are a few of mine:

  • Diplodocoid phylogenetic nomenclature at the Journal of Paleontology, 2004-5 (the first reviews I ever received): three months and 14 days.
  • Revised version of the same paper at PaleoBios, 2005 (my first published paper): one month and 10 days.
  • Xenoposeidon description at Palaeontology, 2006: three months and 19 days, although that included a delay as the handling editor sent it to a third, tie-breaking, reviewer.
  • Brachiosaurus revision at the Journal of Vertebrate Paleontology, 2008: one month and 11 days.
  • Sauropod neck anatomy (eventually to be published in a very different form in PeerJ) at Paleobiologyfive months and two days.
  • Trivial correction to the Brachiosaurus revision at the Journal of Vertebrate Paleontology, 2010: five months and 11 days, bizarrely for a half-page paper.

Despite the wide variations in submission-to-review time at these journals, it’s clear that you can expect to wait at least a month before getting any feedback at all on your submission at traditional journals. Even PeerJ took 19 days to get the reviews of our neck-anatomy paper back to us.

So I am now pretty such sold on the pre-printing route. As well as getting this early version of the paper out there early so that other palaeontologists can benefit from it (and so that we can’t be pre-emptively plagiarised), issuing a preprint has meant that we’ve got really useful feedback very quickly.

I highly recommend this route.

By the way, in case anyone’s wondering, PeerJ Preprints is not only for manuscripts that are destined for PeerJ proper. They’re perfectly happy for you to use their service as a place to gather feedback for your work before submitting it elsewhere. So even if your work is destined for, say, JVP, there’s a lot to be gained by preprinting it first.

What is an ad-hominem attack?

September 4, 2013

I recently handled the revisions on a paper that hopefully will be in press very soon. One of the review comments was “Be very careful not to make ad hominem attacks”.

I was a bit surprised to see that — I wasn’t aware that I’d made any — so I went back over the manuscript, and sure enough, there were no ad homs in there.

There was criticism, though, and I think that’s what the reviewer meant.

Folks, “ad hominem” has a specific meaning. An “ad hominem attack” doesn’t just mean criticising something strongly, it means criticising the author rather than the work. The phrase is Latin for “to the man”. Here’s a pair of examples:

  • “This paper by Wedel is terrible, because the data don’t support the conclusion” — not ad hominem.
  • “Wedel is a terrible scientist, so this paper can’t be trusted” — ad hominem.

What’s wrong with ad hominem criticism? Simply, it’s irrelevant to evaluation of the paper being reviewed. It doesn’t matter (to me as a scientist) whether Wedel strangles small defenceless animals for pleasure in his spare time; what matters is the quality of his work.

Note that ad hominems can also be positive — and they are just as useless there. Here’s another pair of examples:

  • “I recommend publication of Naish’s paper because his work is explained carefully and in detail” — not ad hominem.
  • “I recommend publication of Naish’s paper because he is a careful and detailed worker” — ad hominem.

It makes no difference whether Naish is a careful and detailed worker, or if he always buys his wife flowers on their anniversary, or even if he has a track-record of careful and detailed work. What matters is whether this paper, the one I’m reviewing, is good. That’s all.

As it happens the very first peer-review I ever received — for the paper that eventually became Taylor and Naish (2005) on diplodocoid phylogenetic nomenclature — contained a classic ad hominem, which I’ll go ahead and quote:

It seems to me perfectly reasonable to expect revisers of a major clade to have some prior experience/expertise in the group or in phylogenetic taxonomy before presenting what is intended to be the definitive phylogenetic taxonomy of that group. I do not wish to demean the capabilities of either author – certainly Naish’s “Dinosaurs of the Isle of Wight” is a praiseworthy and useful publication in my opinion – but I question whether he and Taylor can meet their own desiderata of presenting a revised nomenclature that balances elegance, consistency, and stability.

You see what’s happening here? The reviewer was not reviewing the paper, but the authors. There was no need for him or her to question whether we could meet our desiderata: he or she could just have read the manuscript and found out.

(Happy ending: that paper was rejected at the journal we first sent it to, but published at PaleoBios in revised form, and bizarrely is my equal third most-cited paper. I never saw that coming.)

Why giraffes have short necks

September 26, 2012

Today sees the publication, on arXiv (more on that choice in a separate post), of Mike and Matt’s new paper on sauropod neck anatomy. In this paper, we try to figure out why it is that sauropods evolved necks six times longer than that of the world-record giraffe — as shown in Figure 3 from the paper (with a small version of Figure 1 included as a cameo to the same scale):

Figure 3. Necks of long-necked sauropods, to the same scale. Diplodocus, modified from elements in Hatcher (1901, plate 3), represents a “typical” long-necked sauropod, familiar from many mounted skeletons in museums. Puertasaurus modified from Wedel (2007a, figure 4-1). Sauroposeidon scaled from Brachiosaurus artwork by Dmitry Bogdanov, via commons.wikimedia.org (CC-BY-SA). Mamenchisaurus modified from Young and Zhao (1972, figure 4). Supersaurus scaled from Diplodocus, as above. Alternating pink and blue bars are one meter in width. Inset shows Figure 1 to the same scale.

This paper started life as a late-night discussion over a couple of beers, while Matt was over in England for SVPCA back in (I think) 2008. It was originally going to be a short note in PaleoBios, just noting some of the oddities of sauropod cervical architecture — such as the way that cervical ribs, ventral to the centra, elongate posteriorly but their dorsal counterparts the epipophyses do not.

As so often, the tale grew in the telling, so that a paper we’d initially imagined as a two-or-three-page note became Chapter 5 of my dissertation under the sober title of “Vertebral morphology and the evolution of long necks in sauropod dinosaurs”, weighing in at 41 1.5-spaced pages. By now the manuscript had metastatised into a comparison between the necks of sauropods and other animals and an analysis of the factors that enabled sauropods to achieve so much more than mammals, birds, other theropods and pterosaurs.

(At this point we had one of our less satisfactory reviewing experiences. We sent the manuscript to a respected journal, where it wasn’t even sent out to reviewers until more than a month had passed. We then had to repeatedly prod the editor before anything else happened. Eventually, two reviews came back: one of them careful and detailed; but the other, which we’d waited five months for, dismissed our 53-page manuscript in 108 words. So two words per page, or about 2/3 of a word per day of review time. But let’s not dwell on that.)

Figure 6. Basic cervical vertebral architecture in archosaurs, in posterior and lateral views. 1, seventh cervical vertebra of a turkey, Meleagris gallopavo Linnaeus, 1758, traced from photographs by MPT. 2, fifth cervical vertebra of the abelisaurid theropod Majungasaurus crenatissimus Depéret, 1896,UA 8678, traced from O’Connor (2007, figures 8 and 20). In these taxa, the epipophyses and cervical ribs are aligned with the expected vectors of muscular forces. The epipophyses are both larger and taller than the neural spine, as expected based on their mechanical importance. The posterior surface of the neurapophysis is covered by a large rugosity, which is interpreted as an interspinous ligament scar like that of birds (O’Connor, 2007). Because this scar covers the entire posterior surface of the neurapophysis, it leaves little room for muscle attachments to the spine. 3, fifth cervical vertebra of Alligator mississippiensis Daudin, 1801, MCZ 81457, traced from 3D scans by Leon Claessens, courtesy of MCZ. Epipophyses are absent. 4, eighth cervical vertebra of Giraffatitan brancai (Janensch, 1914) paralectotype HMN SII, traced from Janensch (1950, figures 43 and 46). Abbreviations: cr, cervical rib; e, epipophysis; ns, neural spine; poz, postzygapophysis.

This work made its next appearance as my talk at SVPCA 2010 in Cambridge, under the title Why giraffes have such short necks. For the talk, I radically restructured the material into a form that had a stronger narrative — a process that involved a lot of back and forth with Matt, dry-running the talk, and workshopping the order in which ideas were presented. The talk seemed to go down well, and we liked the new structure so much more than the old that we reworked the manuscript into a form that more closely resembled the talk.

That’s the version of the manuscript that we perfected in New York when we should have been at all-you-can-eat sushi places. It’s the version that we submitted on the train from New York to New Haven as we went to visit the collections of the Yale Peabody Museum. And it’s the version that was cursorily rejected from mid-to-low ranked palaeo journal because a reviewer said “The manuscript reads as a long “story” instead of a scientific manuscript” — which was of course precisely what we’d intended.

Needless to say, it was deeply disheartening to have had what we were convinced was a good paper rejected twice from journals, at a cost of three years’ delay, on the basis of these reviews. One option would have been to put the manuscript back into the conventional “scientific paper” straitjacket for the second journal’s benefit. But no. We were not going to invest more work to make the paper less good. We decided to keep it in its current, more readable, form and to find a journal that likes it on that basis.

At the moment, the plan is to send it to PeerJ when that opens to submissions. (Both Matt and I are already members.) But that three-years-and-rolling delay really rankles, and we both felt that it wasn’t serving science to keep the paper locked up until it finally makes it into a journal — hence the deposition in arXiv which we plan to talk about more next time.

Table 3. Neck-elongation features by taxon.

In the paper, we review seven characteristics of sauropod anatomy that facilitated the evolution of long necks: absolutely large body size; quadrupedal stance; proportionally small, light head; large number of  cervical vertebrae; elongation of cervical vertebrae; air-sac system; and vertebral pneumaticity. And we show that giraffes have only two of these seven features. (Ostriches do the next best, with five, but they are defeated by their feeble absolute size.)

The paper incorporates some material from SV-POW! posts, including Sauropods were corn-on-the-cob, not shish kebabs. In fact, come to think of it, we should have cited that post as a source. Oh well. We do cite one SV-POW! post: Darren’s Invading the postzyg, which at the time of writing is the only published-in-any-sense source for pneumaticity invading cervical postzygapogyses from the medial surface.

As for the non-extended epipophyses that kicked the whole project off: we did illustrate how they could look, and discussed why they would seem to make mechanical sense:

Figure 10. Real and speculative muscle attachments in sauropod cervical vertebrae. 1, the second through seventeenth cervical vertebrae of Euhelopus zdanskyi Wiman, 1929 cotype specimen PMU R233a-δ(“Exemplar a”). 2, cervical 14 as it actually exists, with prominent but very short epipophyses and long cervical ribs. 3, cervical 14 as it would appear with short cervical ribs. The long ventral neck muscles would have to attach close to the centrum. 4, speculative version of cervical 14 with the epipophyses extended posteriorly as long bony processes. Such processes would allow the bulk of both the dorsal and ventral neck muscles to be located more posteriorly in the neck, but they are not present in any known sauropod or other non-avian dinosaur. Modified from Wiman (1929, plate 3).

But we found and explained some good reasons why this apparently appealing arrangement would not work. You’ll need to read the paper for details.

Sadly, we were not able to include this slide from the talk illustrating the consequences:

Anyway, go and read the paper! It’s freely available, of course, like all arXiv depositions, and in particular uses the permissive Creative Commons Attribution (CC BY) licence. We have assembled related information over on this page, including full-resolution versions of all the figures.

In the fields of maths, physics and computer science, where deposition in arXiv is ubiquitous, standard practice is to go right ahead and cite works in arXiv as soon as they’re available, rather than waiting for them to appear in journals. We will be happy for the same to happen with our paper: if it contains information that’s of value to you, then feel free to cite the arXiv version.

Reference

  • Taylor, Michael P., and Mathew J. Wedel. 2012. Why sauropods had long necks; and why giraffes have short necks. arXiv:1209.5439. 39 pages, 11 figures, 3 tables. [Full-resolution figures]

How things have always been

Traditional scientific journals ask peer-reviewers to do two things: assess whether a manuscript is scientifically sound, and judge whether it’s sufficiently important to appear in the particular journal it’s been submitted to.

So I could have sent my 2009 paper on Brachiosaurus to Nature, and the reviewers would (presumably) have said “this is good science, but not exciting or sexy enough for Nature“. My article would have been filtered out of Nature, which after all is very limited for space. Instead, I sent it to the Journal of Vertebrate Paleontology, where the exciting-and-sexy bar is calibrated differently, and it passed both halves of the peer-review test.

Enter PLoS

The great insight of PLoS ONE was to recognise the two-pronged nature of peer-review, and to tease them apart by discarding the second prong completely. Its guidelines for reviewers are clear:

Unlike many journals which attempt to use the peer review process to determine whether or not an article reaches the level of ‘importance’ required by a given journal, PLoS ONE uses peer review to determine whether a paper is technically sound and worthy of inclusion in the published scientific record. Once the work is published in PLoS ONE, the broader community is then able to discuss and evaluate the significance of the article (through the number of citations it attracts; the downloads it achieves; the media and blog coverage it receives; and the post-publication Notes, Comments and Ratings that it receives on PLoS ONE etc).

I like to think of this as “kill ’em all and let God sort it out”, but a less colourful description that has caught on is “publish then filter“. This name contrasts nicely with the traditional model, which can be called “filter then publish“.

The models compared

On the whole, traditionalists prefer the older model, because when filtering is done in advance by professionals it saves them from having to do their own filtering.

Or does it?

No.

There was a time when it probably did: when to keep up with a field, it would be sufficient to read (or at least scan) the articles in a handful of the discipline’s top journals. But those days are long gone. I took a random selection of ten PDFs from my own library, and checked what journals they were in. In that sample, only a single journal came up more than once: there were two papers from Acta Paleontologica Polonica. The others were from Acta Geologica Sinica, the Anatomical Record, Animal Behaviour, Comparative Biochemistry and Physiology, Herpetological Conservation and Biology, the Journal of Vertebrate Paleontology and the Quarterly Journal of the Geological Society, plus a dissertation from the University of Flensburg. (And I am one of the most narrowly focussed researchers you could meet.)

In the face of such a flood of information, no-one can read everything that’s made it through the filters into all their favourite journals. So in practice what actually happens is that each of us filters again — finding relevant publications in a huge range of journals by the social web we’re in: mailing lists, blogs, Twitter, and so on. I believe some people even use FaceBook.

A tentative conclusion

So the real choice is between publish-then-filter or filter-then-publish-then-filter.

Put that way, I’m not sure I see very much value in that first filtering phase. I know it’s going to let through a ton of stuff that I don’t care about — all the palaeobotany papers in Palaeontologia Electronica, for example. But that pre-filter is also bound to stop a lot of stuff that I would care about if it were published. If JVP rejects someone’s unexciting paper on a partial Brachiosaurus specimen because it’s not sufficiently exciting, that may be good for the journal’s “prestige” (whatever that means) but it certainly doesn’t serve me as a researcher: I want all known specimens to be published.

So I am coming round to thinking that the PLoS way is best: if a paper is good science, then why even bother thinking about its likely impact? It’s not like that’s something we can expect to guess accurately, anyway. Just publish it and let the ashes fall where they may.  The world will figure out for itself whether it’s worth reading and citing.

… and that’s why we’re angry.

(Note: exact percentages are made up.  But based on a true story.)